i've got the same problem. while i can adjust well for the basic commands, it gets tricky when i have to use the devil ophium or the axe because the bind is set on R3, and clicking R3+X/square is complicated
I found a solution. The problem occurs to those who use Original PS2 controller with USB. Just download an Xbox360 emulator so the game will recognize your controller as it. It works flawlessly then.